We have RNAseq data for ~120 samples.
We are considering of using "Trinity Differential Expression" protocol described by Brian Haas in https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential-Expression
How well does it work without the RSEM abundance of estimation?
We were thinking of feeding normalized gene counts (e.g., by TMM logCPM) into the Trinity protocol.
Thank you very much for your help,